Last night's Dollhouse advanced a theme the show has sneaked into a few episodes so far: The idea that the abusive, mind-crushing Dollhouse is the future of the human race.

Of course, that bit of wisdom comes from the show's "villain," Alpha, who's arguably the most perfect product of the Dollhouse's mind-conditioning technology. Alpha used to be a Doll, just like Echo or Victor, but he had a "composite event," in which all of his different pre-programmed personalities blurred together and he went insane. Now he's fascinated with Echo, the only other Doll who seems to have transcended her programming. When Alpha bust out of the Dollhouse, killing a ton of people along the way, he left two people alive: Dr. Claire Saunders, whose face he scarred, and Echo, whom he left unharmed.

Since then, Alpha has been sending pictures and video of Echo (from before her mind-wiping) to former FBI agent Paul Ballard. And he apparently hired a guy to take Echo out on an engagement and then unexpectedly try to kill her, so she'd be forced to develop new reserves of self-awareness to survive. Then he hacked her cellphone and used to to "reboot" her brain while she was in the middle of a robbery, so she'd be exposed to unusual stresses while in her blank "Doll" state. Apparently, none of these moves had the desired effect, because in last night's episode, Alpha decided to take matters into his own hands.

Alpha killed Stephen Kepler the guy who pretty much designed the Dollhouse (using the most advanced eco-friendly self-sufficiency tech — not because the Dollhouse cares about the environment, but because it wants to be off the grid.) And he took the guy's place, manipulating Paul Ballard into taking him back inside the Dollhouse so he could grab Echo. Ballard, of course, has his own obsession with Echo — partly thanks to Alpha's mind games — and he's convinced he can rescue her from the Dollhouse, and then somehow use her to bring the Dollhouse down. (Wouldn't it have made more sense for Ballard, having located the Dollhouse, to leave and come back with an FBI squad? He could have gotten some vindication.)

So while Alpha is pretending to be the eco-freak Kepler, he spills some insights into what the Dollhouse is, and how it works. And it's not pretty — the Dollhouse is the future of the human race, according to Kepler, because it's so efficient. (Actually, at first, he claims that the human race won't even be around in 200 years, and the planet Earth can have a "humans day" to celebrate our existence by shaking our bones.) But then he says the ultra-efficient Dollhouse really is the future of humanity, because nothing is wasted. And of course, part of that efficiency is that humans are turned into interchangeable cogs instead of the messy, unpredictable individuals we are currently.

And that's the other theme that Dollhouse has been sneaking up on us with: if people are just software running on a particular bit of hardware, then you can swap them out. We saw that last week, with Echo being "loaded" with the mind of a rich dead woman who wanted the only kind of resurrection she could have. And this week, we saw Victor being loaded with the mind of Mr. Dominic, the former Dollhouse head of security who's been "sent to the Attic." (Apparently going to the Attic is serious enough that it's easier to load Dominic on Victor's body than to restore him to his own body. It also gave us the chance to see Enver Gjokag doing a spot-on Reed Diamond impression.) There are only two people for whom this seems not to be true: Alpha and Echo. No wonder Alpha is so obsessed with her.

And it looks like next week, we're going to get the final permutation in the weird brain-freaking maneuvers. Alpha's going to load Caroline's brain into some random woman's body, and then let Caroline meet Echo. Whoah.

The only part of the episode that didn't entirely make sense to me was why Alpha needed Paul Ballard's help to get inside the Dollhouse. Maybe it was a two-person operation: Alpha disables the security systems, while Paul goes and grabs Echo during the confusion. But it still seemed like a mega genius like Alpha could have figured out a way to do it without Paul's help. Maybe he just knew Paul was going to be invading the Dollhouse soon enough, so he figured he'd lend a hand.

Meanwhile, we got the confrontations we've been waiting for, between Ballard and Adelle, and especially Ballard and Boyd Langton. Paul and Boyd seem so similar that you'd think they have to wind up on the same side, and Boyd's been the main voice for the audience's doubts about the Dollhouse for a while now. Really, the only argument the Boyd had to offer in the face of all Paul's righteousness was that you can't simply take the Dolls out of the Dollhouse, because it's not that simple. Adelle, meanwhile, doesn't even make much of an effort to justify herself to Paul, although she does turn it around by accusing him of assaulting one of the Dollhouse's "residents." In the end, though, Boyd is shamed enough to try and hang on to his last sliver of morality. Adelle wants to erase Paul's brain, and Boyd insists that Paul hasn't "consented" to that. It's almost impossible to believe that Boyd still considers the Dollhouse's wholesale erasure of human beings to be consensual, especially after what happened to Dominic, but apparently that's the thin reed he's been clinging to all this time.

The other ethical justification for the Dollhouse, of course, is that it helps people — and we see that in full effect this time around. In another totally bizarre permutation of the Dollhouse's brain science, Echo gets sent to help Susan, an 11-year-old girl who's at risk of all sorts of stuff. She was put out on the streets at a young age and pimped out to whoever wanted her, and now she's a mess. So Topher gets the weird but brilliant idea of taking a brain scan of Susan and updating it to become a healthy adult brain, but with the same memories. And he puts that brain into Echo, then sends her to provide a positive role model. It's totally demented, but also kind of sweet. And of course, Topher's feeling of pride and moral awesomeness lasts exactly five minutes before he's asked to do something morally reprehensible and dehumanizing — who didn't see that coming?

Of course, Echo's way of providing hope to Susan relies on a metaphorical pretzel twist — she tells her the story of Briar Rose, a fairytale princess who gets put under a spell for 100 years, at the end of which a prince comes to rescue her. Susan points out, rightly, that the prince showed up when the spell was about to end anyway, and then takes credit for everything. But Echo says Susan should think of the prince as another aspect of the princess — someone the princess created to rescue herself. Except, of course, that you can't quite negate the existence of another person quite so easily. That's how we got into this mess in the first place. Of course, we're supposed to read that fairytale re-engineering as meaning that Echo somehow drew Paul Ballard there to rescue her, which is a somewhat selective reading of the facts.

All in all, this was another pretty great episode. I had a few minor issues, like the fact that Alan Tudyk overdid the wackiness just a tad when he was playing Alpha-as-Kepler. But it sort of underscored that Alpha and Topher have a lot in common, since Alpha's "nerd" mannerisms were very Topher-esque. More than ever, I'm left wishing that Fox had led Joss Whedon use his original pilot, which set up the show as a tense, twisty thriller about Paul Ballard trying to uncover the truth about the Dollhouse and what it means for the future of the human race. That's what the show has turned into by now, but I suspect a lot of people would have liked it better if it'd been that way from the start. As it is, last night's episode got the worst ratings yet — which means that even if the Dollhouse is our future, its own future isn't so assured.